How do I make a new rest pose when using wieghts and MeshDeform?
There are almost certainly multiple ways to set up a mesh deformer and an armature, and there are things that seem like they should act like mesh deformers but don't really.  Different techniques demand different solutions, so you have to understand your particular model first.

Let's take the example of a model where it is being deformed by a mesh that is being deformed by an armature.  I'll skip local loc/rot/scale-- really, your armature ought to have a root bone so that you don't need to have any local loc/rot/scale on the object level.



1) Select your object that has a mesh deformer modifier.  Copy the modifier and unbind the copy.  Apply the original mesh deform modifier.

2) Select your deformer-- the target of the mesh deform.  Copy the armature modifier.  Apply the first (top) armature modifier.

3) Select your armature.  Apply pose as resting pose.

4) Select the object to be mesh deformed.  Hit the bind button on the (copied) mesh deform modifier.